Abstract
Purpose
Soil management exerts profound impact on the structure and function of the microbiome. Organic practice is believed to positively affect disease suppressiveness compared to conventional systems. While Pseudomonas has been established as a major player in conferring suppressiveness, the impact of farming practices on its diversity at species level has not been conclusively understood. Also, translation of such knowledge into application requires a mechanistic understanding of the mechanism of action of potent biocontrol strains of Pseudomonas.
Methods and results
We compared fields under conventional and organic farming, under long-term (~19 years) management. Profiling of Pseudomonas community structure using rpoD-based amplicon sequencing revealed a higher diversity of known antagonistic Pseudomonas spp. in soils sampled from organic fields compared to conventional field. Cultivation and genome sequencing of selected Pseudomonas isolates from the organic field identified species with multiple secondary metabolite biosynthetic gene clusters and antagonistic activity towards phytopathogens. The selected Pseudomonas isolates showed colonization of wheat root system as confirmed by scanning electron microscopy. In vitro tube assay using wheat also revealed the suppressive activity of potent Pseudomonas isolates against Fusarium oxysporum and Verticillium dahliae. Production of metabolites with antimicrobial activity was verified using untargeted metabolomics (LC/MS).
Conclusions
Overall, the mechanistics involved in the contribution of Pseudomonas spp. to disease suppressiveness in the field under organic farming could be established. This study reports that microbiome from organic field exhibits enhanced diversity of antagonistic Pseudomonas spp. effective against phytopathogens, compared to the conventional practice, and has the potential to promote sustainable agriculture and disease management.
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Acknowledgments
We would like to thank Jonas Greve Lauritsen for help with data analysis of Pseudomonas metagenomics and whole-genome sequencing. We are also grateful to Mario Wibowo for his assistance in carrying out the LC/MS experiments, and Annapurna Bhattacharjee for help with in vitro tube assay.
Funding
The authors would like to thank IIT Delhi and ICAR for providing financial assistance under the M-FIRP scheme (MI02024). We would also like to acknowledge the Danish National Research Foundation (DNRF137) for providing funding to the Center for Microbial Secondary Metabolites. SK received an exchange fellowship from Novozymes and the Henning Holck–Larsen Foundation. SK received fellowship from University Grants Commission (UGC) India.
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Khatri, S., Sazinas, P., Strube, M.L. et al. Pseudomonas is a key player in conferring disease suppressiveness in organic farming. Plant Soil (2023). https://doi.org/10.1007/s11104-023-05927-6
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DOI: https://doi.org/10.1007/s11104-023-05927-6